The present application generally relates to optimization-based control methods and control systems for diesel engines including an air handling system, and more particularly to controlling air handling system actuators in such systems. For diesel engines, an insufficient amount of air may lead to an increase in particulate emissions, while an excess of air and low amount of recirculated exhaust gas may lead to an increase in NOx emissions. Present approaches to controls for such systems suffer from a number of limitations and shortcomings. Therefore, a need remains for further improvements in systems, apparatus, and methods for controlling air handling actuators.